When foreign bodies (usually bacteria or viruses) enter the bloodstream, they are taken up by antigen-presenting cells (APCs) such as macrophages. The macrophages then break down the bacteria or viruses or whatever and incorporate their composite proteins, called antigens, into proteins called major histocompatibility complex class II (MHC-II) proteins. These MHC-II proteins are then sent to the cell membrane, where they present the antigens to T cells. The T cells determine whether the proteins presented are compatible with known "self" protein complexes and, upon recognizing the protein as foreign, induce other T cells to pick up and destroy the invading body. The T cells also stimulate B cells to produce antibodies to those antigens, so that subsequent infection attempts will be thwarted.

In more technical terms, the epitope is the part of the antigen that is recognized by the T cell and the antibody in order for a reaction to occur. Therefore, it is the epitope which lends the antigenic property to the antigen. Most antigens actually carry numerous epitopes of all sorts, providing the potential for multiple various antibodies to bind them. This duplication usually results in a faster antibody response than would occur if only one epitope was recognized on any single foreign body.

Once the protein has been tagged, visualization studies are executed; this usually involves gelelectrophoresis, mobility assays, ELISA, affinitychromatography, Western blotting, or immunofluorescence assays. The protein can also be introduced to cells in vitro for functional and binding assays, especially when tagged with dyes or small molecules. In any of these cases, the proteins are exposed to pre-made antibodies for the epitope being used (usually purchased in conjunction with the epitope construct), and the antibody-epitope binding reaction results in some form of indication of the presence of the protein (stain, fluorescent emission, chemical emission, etc.). For example, Western blotting involves probing for the protein with the antibody, then counter-binding with a dye that binds to the antibody-protein complex. biotinylated proteins, usually used in ELISA and similar assays, are usually found through the use of avidin, which is a protein that has a very high affinity for biotin; the avidin is usually bound to another protein that catalyzes an indicator reaction, resulting in a color gradient representative of the amount of protein present.

Tagging proteins is often useful when no epitopes are known to be found on the protein in question, and especially if the protein is novel. Without the use of an epitope tag, an antibody would have to be generated in order to track the protein. This process is best described as a long, arduous, and rarely successful journey. However, to engineer an epitope sequence into a protein does not even require a full gene sequence; rather, only a short known coding region is necessary to insert the epitope-tag DNA sequence into the protein. The protein can then be followed in the cell, as the epitope tag will be carried with the protein. The virtue of this procedure lies in its versatility with reference to novel proteins; genome-sequencing projects in yeast, plants, and humans has resulted in thousands of coding regions whose functions within the cell and the organism are unknown. in vitro translation studies and the use of epitope tagging techniques promises to provide some answers to the questions arising from these new sequences.

a noder says re epitope: So these epitopes being mistakenly associated with the body's own proteins would lead to autoimmune disorders?

No.

When the epitopes on foreign antigens are recognized as "self", no reaction to the foreign body is elicited. This is a horrible effect called immunosuppression, which can lead to some very icky diseases taking over your system. This is the short version of what can happen to people who have advanced AIDS (because they have no T cells to recognize antigen) or are on immunosuppressive therapies after transplants (because the MHC proteins are blocked by drugs). For this reason, the immune system has evolved a serious checking system wherein it recognizes multiple thousands of different epitopes, so that in theory it will catch one foreign epitope on any given foreign body.

On the other hand, "self" proteins can be recognized as foreign in cases of autoimmune disorders, such as diabetes mellitus, lupus, and MS. In all of these disorders, certain proteins in the body are attacked by the immune system because they fail to recognize the "self" epitope tags on the antigens expressed on the surface of their tissues. Many people who suffer from these disorders are forced to maintain an immunosuppressive therapeutic regimen as their disorders progress.